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Summarize all MCP tools, capabilities, and usage examples for this project
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Based on SOC occupation classification
Full clinical variant workup — gnomAD population frequency, ClinVar significance, protein domain impact, AlphaFold structure context, and PubMed literature
Compare a gene across multiple species — find orthologs, retrieve sequences, compute alignments, and summarize conservation
Druggability assessment — protein function, 3D structures, ligand-bound PDBs, binding sites, interaction network, disease associations, and literature
Functional analysis of a gene list — batch summaries, pathway mapping, protein interactions, tissue expression, and phenotype associations
Generate a comprehensive gene report by combining data from NCBI, Ensembl, UniProt, ClinVar, PDB, InterPro, STRING, and KEGG
Research session lab notebook — start, annotate, update, report, or check status
| name | project-summary |
| description | Summarize all MCP tools, capabilities, and usage examples for this project |
Read the file PROJECT_INVENTORY.md from the project root and present a formatted summary including:
datasets_summary_gene with symbol BRCA1 and taxon humansequence_align with two protein sequencesensembl_lookup_gene with symbol TP53uniprot_search for BRCA1 in humanclinvar_search for pathogenic BRCA1 variantspdb_search for TP53 structuresstring_get_interactions for TP53blast_search with a protein sequencepubmed_search for CRISPR gene therapy papersalphafold_get_prediction for P04637/project-summary, /gene-report <gene> (comprehensive multi-database gene report), /variant-report <target> (variant annotation report), /protein-report <protein> (protein-centric report with structure, PTMs, interactions, expression), /pathway-report <pathway> (pathway deep-dive with Reactome data, member genes, clinical variants, literature), /drug-target-report <target> (druggability assessment with structures, binding sites, disease rationale, COSMIC mutations), and /lab-notebook <subcommand> (research session lab notebook — start, annotate, update, report, status)
/literature-agent <topic> (PubMed literature search and summary), /comparative-genomics-agent <gene> <species...> (multi-species gene comparison with alignments), /clinical-variant-agent <variant> (full variant workup), /gene-list-agent <genes> (functional analysis of a gene list), /structure-agent <target> (structural biology deep-dive with all PDB structures, AlphaFold, variant mapping), /statistical-methods-agent <paper> (paper statistical analysis — fetches full text, inventories every statistical method, critiques assumptions and appropriateness)Keep the output concise and well-formatted with markdown.